# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 17:24:34 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-[(4~{Z})-2-(aminomethyl)-4-(1~{H}-indol-3-ylmethylidene)-5-oxidanylidene-imidazol-1-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1=NC(=C\c2c[nH]c3ccccc23)/C(=O)N1CC(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 IO8  IO8  "2-[2-(aminomethyl)-4-(1H-indol-3-ylmethyl)-5-oxidanylidene-4H-imidazol-1-yl]ethanoic acid"  L-peptide  35  22  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_IO8
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 IO8  C1   C  CR5    0   0.510  -13.1816  26.3594  -26.5690
 IO8  O2   O  O      0  -0.465  -15.4702  28.4364  -25.1386
 IO8  C2   C  CR5    0   0.507  -14.8029  27.5127  -25.5698
 IO8  C    C  C      0   0.416  -13.4390  29.2629  -28.0152
 IO8  CD2  C  CR5    0  -0.009  -16.1945  22.9042  -25.5112
 IO8  CE3  C  C1     0  -0.385  -15.0327  22.4615  -26.1536
 IO8  CZ3  C  C1     0  -0.255  -14.8858  21.1137  -26.4244
 IO8  CH2  C  C1     0  -0.279  -15.8734  20.1839  -26.0702
 IO8  CZ2  C  C1     0  -0.296  -17.0314  20.5885  -25.4353
 IO8  CE2  C  CR5    0   0.348  -17.1704  21.9460  -25.1652
 IO8  NE1  N  NR15   0  -0.677  -18.2062  22.6033  -24.5507
 IO8  CD1  C  CR15   0  -0.019  -17.9339  23.9181  -24.4922
 IO8  CG   C  CR5    0   0.078  -16.7033  24.1852  -25.0687
 IO8  CB   C  C1     0  -0.414  -16.2159  25.5279  -25.1213
 IO8  CA2  C  CR5    0   0.068  -15.0835  26.0648  -25.6259
 IO8  N2   N  N      0  -0.486  -14.0258  25.4329  -26.2686
 IO8  N    N  NR5    0  -0.523  -13.5552  27.6156  -26.1436
 IO8  CA   C  CH2    0  -0.479  -12.9915  28.8656  -26.5852
 IO8  O    O  O      0  -0.601  -13.0279  30.3738  -28.3918
 IO8  CA1  C  CH2    0  -0.407  -11.8772  26.1116  -27.2499
 IO8  N1   N  NH2    0  -0.795  -10.7873  26.1193  -26.2790
 IO8  OXT  O  OC    -1  -0.587  -14.1417  28.4448  -28.6312
 IO8  H3   H  H      0   0.251  -15.7283  19.1357  -26.2971
 IO8  H4   H  H      0   0.263  -17.8014  19.8799  -25.1582
 IO8  H5   H  HNR5   0   0.419  -19.0457  22.1698  -24.1999
 IO8  H6   H  HCR5   0   0.302  -18.6284  24.6121  -24.0441
 IO8  H7   H  H      0   0.262  -16.8881  26.2543  -24.6727
 IO8  HA2  H  HCH2   0   0.263  -11.9015  28.8174  -26.5419
 IO8  HA3  H  HCH2   0   0.267  -13.2851  29.6410  -25.8766
 IO8  H12  H  HCH2   0   0.261  -11.9346  25.1191  -27.6958
 IO8  H13  H  HCH2   0   0.232  -11.7558  26.8253  -28.0734
 IO8  H14  H  HNH2   0   0.360   -9.9415  25.8151  -26.7443
 IO8  HN2  H  HNH2   0   0.350  -10.6008  27.0654  -25.9707
 IO8  H1   H  H      0   0.272  -14.2681  23.1725  -26.4308
 IO8  H2   H  H      0   0.246  -13.9881  20.7673  -26.9206

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 IO8  C    O    deloc     1.243  0.020  1.243
 IO8  C    CA   single    1.550  0.020  1.550
 IO8  CA1  C1   single    1.492  0.020  1.492
 IO8  CA1  N1   single    1.460  0.020  1.460
 IO8  C1   N2   double    1.289  0.020  1.289
 IO8  C1   N    single    1.378  0.020  1.378
 IO8  N2   CA2  single    1.390  0.020  1.390
 IO8  CA   N    single    1.441  0.020  1.441
 IO8  CZ3  CE3  aromatic  1.383  0.020  1.383
 IO8  CZ3  CH2  aromatic  1.402  0.020  1.402
 IO8  N    C2   single    1.377  0.020  1.377
 IO8  CE3  CD2  aromatic  1.399  0.020  1.399
 IO8  CA2  C2   single    1.476  0.020  1.476
 IO8  CA2  CB   double    1.351  0.020  1.351
 IO8  CH2  CZ2  aromatic  1.381  0.020  1.381
 IO8  C2   O2   double    1.218  0.020  1.218
 IO8  CB   CG   single    1.429  0.020  1.429
 IO8  CD2  CG   aromatic  1.448  0.020  1.448
 IO8  CD2  CE2  aromatic  1.411  0.020  1.411
 IO8  CG   CD1  aromatic  1.385  0.020  1.385
 IO8  CZ2  CE2  aromatic  1.391  0.020  1.391
 IO8  CE2  NE1  aromatic  1.372  0.020  1.372
 IO8  CD1  NE1  aromatic  1.344  0.020  1.344
 IO8  C    OXT  deloc     1.242  0.020  1.242
 IO8  CE3  H1   single    0.930  0.020  1.080
 IO8  CZ3  H2   single    0.930  0.020  1.080
 IO8  CH2  H3   single    0.930  0.020  1.080
 IO8  CZ2  H4   single    0.930  0.020  1.080
 IO8  NE1  H5   single    0.860  0.020  1.020
 IO8  CD1  H6   single    0.930  0.020  1.080
 IO8  CB   H7   single    0.930  0.020  1.080
 IO8  CA   HA2  single    0.970  0.020  1.090
 IO8  CA   HA3  single    0.970  0.020  1.090
 IO8  CA1  H12  single    0.970  0.020  1.090
 IO8  CA1  H13  single    0.970  0.020  1.090
 IO8  N1   H14  single    0.890  0.020  1.040
 IO8  N1   HN2  single    0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 IO8  CA1  C1   N    121.96  3.000
 IO8  N    C1   N2   113.94  3.000
 IO8  CA1  C1   N2   124.03  3.000
 IO8  N    C2   CA2  103.28  3.000
 IO8  CA2  C2   O2   130.78  3.000
 IO8  N    C2   O2   125.94  3.000
 IO8  OXT  C    O    128.73  3.000
 IO8  OXT  C    CA   116.87  3.000
 IO8  O    C    CA   114.40  3.000
 IO8  CG   CD2  CE2  106.44  3.000
 IO8  CE2  CD2  CE3  118.17  3.000
 IO8  CG   CD2  CE3  135.40  3.000
 IO8  H1   CE3  CZ3  121.07  3.000
 IO8  H1   CE3  CD2  119.81  3.000
 IO8  CZ3  CE3  CD2  119.11  3.000
 IO8  H2   CZ3  CH2  119.20  3.000
 IO8  H2   CZ3  CE3  119.33  3.000
 IO8  CH2  CZ3  CE3  121.48  3.000
 IO8  H3   CH2  CZ2  119.50  3.000
 IO8  H3   CH2  CZ3  119.66  3.000
 IO8  CZ2  CH2  CZ3  120.83  3.000
 IO8  H4   CZ2  CE2  121.20  3.000
 IO8  H4   CZ2  CH2  121.48  3.000
 IO8  CE2  CZ2  CH2  117.32  3.000
 IO8  NE1  CE2  CZ2  129.04  3.000
 IO8  NE1  CE2  CD2  107.86  3.000
 IO8  CZ2  CE2  CD2  123.09  3.000
 IO8  H5   NE1  CD1  125.06  3.000
 IO8  H5   NE1  CE2  125.36  3.000
 IO8  CD1  NE1  CE2  109.59  3.000
 IO8  H6   CD1  CG   128.36  3.000
 IO8  H6   CD1  NE1  121.11  3.000
 IO8  CG   CD1  NE1  110.52  3.000
 IO8  CB   CG   CD1  119.96  3.000
 IO8  CD1  CG   CD2  105.60  3.000
 IO8  CB   CG   CD2  134.44  3.000
 IO8  H7   CB   CA2  114.01  3.000
 IO8  H7   CB   CG   113.69  3.000
 IO8  CA2  CB   CG   132.29  3.000
 IO8  N2   CA2  CB   129.05  3.000
 IO8  CB   CA2  C2   122.35  3.000
 IO8  N2   CA2  C2   108.60  3.000
 IO8  CA2  N2   C1   106.23  3.000
 IO8  CA   N    C2   123.17  3.000
 IO8  C2   N    C1   107.83  3.000
 IO8  CA   N    C1   126.18  3.000
 IO8  HA3  CA   HA2  105.93  3.000
 IO8  HA3  CA   N    108.20  3.000
 IO8  HA2  CA   N    109.88  3.000
 IO8  HA3  CA   C    109.84  3.000
 IO8  HA2  CA   C    109.63  3.000
 IO8  N    CA   C    113.09  3.000
 IO8  H13  CA1  H12  106.94  3.000
 IO8  H13  CA1  N1   114.43  3.000
 IO8  H12  CA1  N1   108.44  3.000
 IO8  H13  CA1  C1   109.36  3.000
 IO8  H12  CA1  C1   106.97  3.000
 IO8  N1   CA1  C1   110.39  3.000
 IO8  HN2  N1   H14  105.47  3.000
 IO8  HN2  N1   CA1  110.19  3.000
 IO8  H14  N1   CA1  108.46  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 IO8  CONST_01  CH2  CZ3  CE3  CD2     0.00   0.0  0
 IO8  CONST_02  NE1  CD1  CG   CD2     0.00   0.0  0
 IO8  CONST_03  CH2  CZ2  CE2  CD2     0.00   0.0  0
 IO8  CONST_04  CD1  NE1  CE2  CD2     0.00   0.0  0
 IO8  CONST_05  CZ2  CH2  CZ3  CE3     0.00   0.0  0
 IO8  CONST_06  CD1  CG   CD2  CE3   180.00   0.0  0
 IO8  CONST_07  CZ2  CE2  CD2  CE3     0.00   0.0  0
 IO8  CONST_08  NE1  CE2  CD2  CE3   180.00   0.0  0
 IO8  CONST_09  CG   CD2  CE3  CZ3   180.00   0.0  0
 IO8  CONST_10  CE2  CD2  CE3  CZ3     0.00   0.0  0
 IO8  CONST_11  CE2  CZ2  CH2  CZ3     0.00   0.0  0
 IO8  CONST_12  NE1  CE2  CZ2  CH2   180.00   0.0  0
 IO8  CONST_13  CG   CD2  CE2  CZ2   180.00   0.0  0
 IO8  CONST_14  CD1  NE1  CE2  CZ2   180.00   0.0  0
 IO8  CONST_15  CD1  CG   CD2  CE2     0.00   0.0  0
 IO8  CONST_16  CG   CD1  NE1  CE2     0.00   0.0  0
 IO8  CONST_17  CG   CD2  CE2  NE1     0.00   0.0  0
 IO8  CONST_18  C2   CA2  N2   C1      0.00   0.0  0
 IO8  CONST_19  CA2  C2   N    C1      0.00   0.0  0
 IO8  CONST_20  N2   C1   N    C2      0.00   0.0  0
 IO8  CONST_21  N    C1   N2   CA2     0.00   0.0  0
 IO8  CONST_22  N    C2   CA2  N2      0.00   0.0  0
 IO8  CONST_23  CB   CG   CD2  CE3     0.00   0.0  0
 IO8  CONST_24  CB   CG   CD2  CE2   180.00   0.0  0
 IO8  CONST_25  CB   CG   CD1  NE1   180.00   0.0  0
 IO8  CONST_26  O2   C2   N    C1    180.00   0.0  0
 IO8  CONST_27  CA1  C1   N    C2    180.00   0.0  0
 IO8  CONST_28  CA1  C1   N2   CA2   180.00   0.0  0
 IO8  CONST_29  CA   N    C2   CA2   180.00   0.0  0
 IO8  CONST_31  H2   CZ3  CE3  CD2   180.00   0.0  0
 IO8  CONST_32  H6   CD1  CG   CD2   180.00   0.0  0
 IO8  CONST_33  H4   CZ2  CE2  CD2   180.00   0.0  0
 IO8  CONST_34  H5   NE1  CE2  CD2   180.00   0.0  0
 IO8  CONST_35  H3   CH2  CZ3  CE3   180.00   0.0  0
 IO8  CONST_36  H4   CZ2  CH2  CZ3   180.00   0.0  0
 IO8  CONST_37  H1   CE3  CZ3  CH2   180.00   0.0  0
 IO8  CONST_38  H2   CZ3  CH2  CZ2   180.00   0.0  0
 IO8  CONST_39  H5   NE1  CE2  CZ2     0.00   0.0  0
 IO8  CONST_40  H1   CE3  CD2  CE2   180.00   0.0  0
 IO8  CONST_41  H3   CH2  CZ2  CE2   180.00   0.0  0
 IO8  CONST_42  H6   CD1  NE1  CE2   180.00   0.0  0
 IO8  CONST_43  H4   CZ2  CE2  NE1     0.00   0.0  0
 IO8  CONST_44  H1   CE3  CD2  CG      0.00   0.0  0
 IO8  CONST_45  H5   NE1  CD1  CG    180.00   0.0  0
 IO8  CONST_46  CA   N    C2   O2      0.00   0.0  0
 IO8  Var_01    CG   CB   CA2  C2    179.46   0.0  2
 IO8  Var_02    N2   CA2  CB   CG      0.18   0.0  2
 IO8  Var_03    CA2  CB   CG   CD2     0.46  30.0  3
 IO8  Var_04    CA2  CB   CG   CD1  -179.21  30.0  3
 IO8  Var_05    C    CA   N    C1     74.02  30.0  1
 IO8  Var_06    C    CA   N    C2    -84.59  30.0  1
 IO8  Var_07    N1   CA1  C1   N2   -100.59  30.0  2
 IO8  Var_08    N1   CA1  C1   N      76.02  30.0  2
 IO8  Var_09    H7   CB   CA2  C2     -0.26   0.0  2
 IO8  Var_10    H7   CB   CA2  N2   -179.54   0.0  2
 IO8  Var_11    HA2  CA   N    C1    -48.85  30.0  1
 IO8  Var_12    HA3  CA   N    C1   -164.07  30.0  1
 IO8  Var_13    HA2  CA   N    C2    152.54  30.0  1
 IO8  Var_14    HA3  CA   N    C2     37.32  30.0  1
 IO8  Var_15    H7   CB   CG   CD2  -179.82  30.0  3
 IO8  Var_16    H7   CB   CG   CD1     0.51  30.0  3
 IO8  Var_17    H12  CA1  C1   N2     17.20  30.0  2
 IO8  Var_18    H13  CA1  C1   N2    132.67  30.0  2
 IO8  Var_19    H12  CA1  C1   N    -166.19  30.0  2
 IO8  Var_20    H13  CA1  C1   N     -50.71  30.0  2
 IO8  Var_21    O    C    CA   N     176.12  30.0  3
 IO8  Var_22    OXT  C    CA   N      -4.31  30.0  3
 IO8  Var_23    H14  N1   CA1  C1    171.74  30.0  3
 IO8  Var_24    HN2  N1   CA1  C1    -73.27  30.0  3
 IO8  Var_25    HA2  CA   C    O     -60.88  30.0  3
 IO8  Var_26    HA3  CA   C    O      55.13  30.0  3
 IO8  Var_27    HA2  CA   C    OXT   118.69  30.0  3
 IO8  Var_28    HA3  CA   C    OXT  -125.30  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 IO8  plan-1  C1   0.020
 IO8  plan-1  O2   0.020
 IO8  plan-1  C2   0.020
 IO8  plan-1  CG   0.020
 IO8  plan-1  CB   0.020
 IO8  plan-1  CA2  0.020
 IO8  plan-1  N2   0.020
 IO8  plan-1  N    0.020
 IO8  plan-1  CA   0.020
 IO8  plan-1  CA1  0.020
 IO8  plan-1  H7   0.020
 IO8  plan-2  CD2  0.020
 IO8  plan-2  CE3  0.020
 IO8  plan-2  CZ3  0.020
 IO8  plan-2  CH2  0.020
 IO8  plan-2  CZ2  0.020
 IO8  plan-2  CE2  0.020
 IO8  plan-2  NE1  0.020
 IO8  plan-2  CD1  0.020
 IO8  plan-2  CG   0.020
 IO8  plan-2  CB   0.020
 IO8  plan-2  H3   0.020
 IO8  plan-2  H4   0.020
 IO8  plan-2  H5   0.020
 IO8  plan-2  H6   0.020
 IO8  plan-2  H1   0.020
 IO8  plan-2  H2   0.020
 IO8  plan-3  C    0.020
 IO8  plan-3  CA   0.020
 IO8  plan-3  O    0.020
 IO8  plan-3  OXT  0.020

